*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief Implements gmx dump utility.
+ *
+ * \ingroup module_tools
+ */
#include "gmxpre.h"
#include "dump.h"
#include <cstdio>
#include <cstring>
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/mtxio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxpreprocess/gmxcpp.h"
-#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/math/vecdump.h"
-#include "gromacs/mdrunutility/mdmodules.h"
+#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/txtdump.h"
-static void list_tpx(const char *fn,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters,
- const char *mdpfn,
- gmx_bool bSysTop,
- gmx_bool bOriginalInputrec)
+namespace gmx
{
- FILE *gp;
- int indent, i, j, **gcount, atot;
- t_state state;
- t_tpxheader tpx;
- gmx_mtop_t mtop;
- gmx_groups_t *groups;
- t_topology top;
-
- read_tpxheader(fn, &tpx, TRUE);
- t_inputrec ir;
- read_tpx_state(fn,
- tpx.bIr ? &ir : nullptr,
- &state,
- tpx.bTop ? &mtop : nullptr);
+
+namespace
+{
+
+//! Dump a TPR file
+void list_tpr(const char* fn,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters,
+ const char* mdpfn,
+ gmx_bool bSysTop,
+ gmx_bool bOriginalInputrec)
+{
+ FILE* gp;
+ int indent, atot;
+ t_state state;
+ gmx_mtop_t mtop;
+ t_topology top;
+
+ TpxFileHeader tpx = readTpxHeader(fn, true);
+ t_inputrec ir;
+
+ read_tpx_state(fn, tpx.bIr ? &ir : nullptr, &state, tpx.bTop ? &mtop : nullptr);
if (tpx.bIr && !bOriginalInputrec)
{
- gmx::MDModules().adjustInputrecBasedOnModules(&ir);
+ MDModules().adjustInputrecBasedOnModules(&ir);
}
if (mdpfn && tpx.bIr)
pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
/*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
/*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
- pr_rvecs(stdout, indent, "x", tpx.bX ? as_rvec_array(state.x.data()) : nullptr, state.natoms);
- pr_rvecs(stdout, indent, "v", tpx.bV ? as_rvec_array(state.v.data()) : nullptr, state.natoms);
+ pr_rvecs(stdout, indent, "x", tpx.bX ? state.x.rvec_array() : nullptr, state.natoms);
+ pr_rvecs(stdout, indent, "v", tpx.bV ? state.v.rvec_array() : nullptr, state.natoms);
}
- groups = &mtop.groups;
+ const SimulationGroups& groups = mtop.groups;
- snew(gcount, egcNR);
- for (i = 0; (i < egcNR); i++)
+ gmx::EnumerationArray<SimulationAtomGroupType, std::vector<int>> gcount;
+ for (auto group : keysOf(gcount))
{
- snew(gcount[i], groups->grps[i].nr);
+ gcount[group].resize(groups.groups[group].size());
}
- for (i = 0; (i < mtop.natoms); i++)
+ for (int i = 0; (i < mtop.natoms); i++)
{
- for (j = 0; (j < egcNR); j++)
+ for (auto group : keysOf(gcount))
{
- gcount[j][ggrpnr(groups, j, i)]++;
+ gcount[group][getGroupType(groups, group, i)]++;
}
}
printf("Group statistics\n");
- for (i = 0; (i < egcNR); i++)
+ for (auto group : keysOf(gcount))
{
atot = 0;
- printf("%-12s: ", gtypes[i]);
- for (j = 0; (j < groups->grps[i].nr); j++)
+ printf("%-12s: ", shortName(group));
+ for (const auto& entry : gcount[group])
{
- printf(" %5d", gcount[i][j]);
- atot += gcount[i][j];
+ printf(" %5d", entry);
+ atot += entry;
}
printf(" (total %d atoms)\n", atot);
- sfree(gcount[i]);
}
- sfree(gcount);
}
}
-static void list_top(const char *fn)
+//! Dump a topology file
+void list_top(const char* fn)
{
- int status, done;
-#define BUFLEN 256
- char buf[BUFLEN];
+ int status, done;
+ // Legacy string length macro
+ char buf[STRLEN];
gmx_cpp_t handle;
- char *cppopts[] = { nullptr };
+ char* cppopts[] = { nullptr };
status = cpp_open_file(fn, &handle, cppopts);
if (status != 0)
}
do
{
- status = cpp_read_line(&handle, BUFLEN, buf);
- done = (status == eCPP_EOF);
+ status = cpp_read_line(&handle, STRLEN, buf);
+ done = static_cast<int>(status == eCPP_EOF);
if (!done)
{
if (status != eCPP_OK)
printf("%s\n", buf);
}
}
- }
- while (!done);
+ } while (done == 0);
status = cpp_close_file(&handle);
if (status != eCPP_OK)
{
}
}
-static void list_trr(const char *fn)
+//! Dump a TRR file
+void list_trr(const char* fn)
{
- t_fileio *fpread;
- int nframe, indent;
- char buf[256];
- rvec *x, *v, *f;
- matrix box;
- gmx_trr_header_t trrheader;
- gmx_bool bOK;
+ t_fileio* fpread;
+ int nframe, indent;
+ char buf[256];
+ rvec * x, *v, *f;
+ matrix box;
+ gmx_trr_header_t trrheader;
+ gmx_bool bOK;
- fpread = gmx_trr_open(fn, "r");
+ fpread = gmx_trr_open(fn, "r");
nframe = 0;
while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
snew(x, trrheader.natoms);
snew(v, trrheader.natoms);
snew(f, trrheader.natoms);
- if (gmx_trr_read_frame_data(fpread, &trrheader,
+ if (gmx_trr_read_frame_data(fpread,
+ &trrheader,
trrheader.box_size ? box : nullptr,
- trrheader.x_size ? x : nullptr,
- trrheader.v_size ? v : nullptr,
- trrheader.f_size ? f : nullptr))
+ trrheader.x_size ? x : nullptr,
+ trrheader.v_size ? v : nullptr,
+ trrheader.f_size ? f : nullptr))
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e lambda=%10g\n",
- trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
+ fprintf(stdout,
+ "natoms=%10d step=%10" PRId64 " time=%12.7e lambda=%10g\n",
+ trrheader.natoms,
+ trrheader.step,
+ trrheader.t,
+ trrheader.lambda);
if (trrheader.box_size)
{
pr_rvecs(stdout, indent, "box", box, DIM);
}
else
{
- fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
- nframe, trrheader.t);
+ fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n", nframe, trrheader.t);
}
sfree(x);
}
if (!bOK)
{
- fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
- nframe, trrheader.t);
+ fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n", nframe, trrheader.t);
}
gmx_trr_close(fpread);
}
-static void list_xtc(const char *fn)
+//! Dump an xtc file
+void list_xtc(const char* fn)
{
- t_fileio *xd;
- int indent;
- char buf[256];
- rvec *x;
- matrix box;
- int nframe, natoms;
- int64_t step;
- real prec, time;
- gmx_bool bOK;
+ t_fileio* xd;
+ int indent;
+ char buf[256];
+ rvec* x;
+ matrix box;
+ int nframe, natoms;
+ int64_t step;
+ real prec, time;
+ gmx_bool bOK;
xd = open_xtc(fn, "r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n",
- natoms, step, time, prec);
+ fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n", natoms, step, time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
- }
- while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
+ } while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK) != 0);
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
close_xtc(xd);
}
+#if GMX_USE_TNG
+
/*! \brief Callback used by list_tng_for_gmx_dump. */
-static void list_tng_inner(const char *fn,
- gmx_bool bFirstFrame,
- real *values,
- int64_t step,
- double frame_time,
- int64_t n_values_per_frame,
- int64_t n_atoms,
- real prec,
- int64_t nframe,
- char *block_name)
+void list_tng_inner(const char* fn,
+ gmx_bool bFirstFrame,
+ real* values,
+ int64_t step,
+ double frame_time,
+ int64_t n_values_per_frame,
+ int64_t n_atoms,
+ real prec,
+ int64_t nframe,
+ char* block_name)
{
- char buf[256];
- int indent = 0;
+ char buf[256];
+ int indent = 0;
if (bFirstFrame)
{
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10" PRId64 " step=%10" PRId64 " time=%12.7e",
- n_atoms, step, frame_time);
+ fprintf(stdout, "natoms=%10" PRId64 " step=%10" PRId64 " time=%12.7e", n_atoms, step, frame_time);
if (prec > 0)
{
fprintf(stdout, " prec=%10g", prec);
pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
}
-static void list_tng(const char gmx_unused *fn)
+#endif
+
+//! Dump a TNG file
+void list_tng(const char* fn)
{
-#ifdef GMX_USE_TNG
+#if GMX_USE_TNG
gmx_tng_trajectory_t tng;
int64_t nframe = 0;
int64_t i, *block_ids = nullptr, step, ndatablocks;
gmx_bool bOK;
- real *values = nullptr;
+ real* values = nullptr;
gmx_tng_open(fn, 'r', &tng);
gmx_print_tng_molecule_system(tng, stdout);
- bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
- 0,
- nullptr,
- &step, &ndatablocks,
- &block_ids);
+ bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1, 0, nullptr, &step, &ndatablocks, &block_ids);
do
{
for (i = 0; i < ndatablocks; i++)
{
- double frame_time;
- real prec;
- int64_t n_values_per_frame, n_atoms;
- char block_name[STRLEN];
-
- gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
- &step, &frame_time,
- &n_values_per_frame, &n_atoms,
+ double frame_time;
+ real prec;
+ int64_t n_values_per_frame, n_atoms;
+ char block_name[STRLEN];
+
+ gmx_get_tng_data_next_frame_of_block_type(tng,
+ block_ids[i],
+ &values,
+ &step,
+ &frame_time,
+ &n_values_per_frame,
+ &n_atoms,
&prec,
- block_name, STRLEN, &bOK);
+ block_name,
+ STRLEN,
+ &bOK);
if (!bOK)
{
/* Can't write any output because we don't know what
}
else
{
- list_tng_inner(fn, (0 == i), values, step, frame_time,
- n_values_per_frame, n_atoms, prec, nframe, block_name);
+ list_tng_inner(
+ fn, (0 == i), values, step, frame_time, n_values_per_frame, n_atoms, prec, nframe, block_name);
}
}
nframe++;
- }
- while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
- 0,
- nullptr,
- &step,
- &ndatablocks,
- &block_ids));
+ } while (gmx_get_tng_data_block_types_of_next_frame(
+ tng, step, 0, nullptr, &step, &ndatablocks, &block_ids));
if (block_ids)
{
}
sfree(values);
gmx_tng_close(&tng);
+#else
+ GMX_UNUSED_VALUE(fn);
#endif
}
-static void list_trx(const char *fn)
+//! Dump a trajectory file
+void list_trx(const char* fn)
{
switch (fn2ftp(fn))
{
- case efXTC:
- list_xtc(fn);
- break;
- case efTRR:
- list_trr(fn);
- break;
- case efTNG:
- list_tng(fn);
- break;
+ case efXTC: list_xtc(fn); break;
+ case efTRR: list_trr(fn); break;
+ case efTNG: list_tng(fn); break;
default:
- fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
- fn, fn);
+ fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n", fn, fn);
}
}
-static void list_ene(const char *fn)
+//! Dump an energy file
+void list_ene(const char* fn)
{
- ener_file_t in;
- gmx_bool bCont;
- gmx_enxnm_t *enm = nullptr;
- t_enxframe *fr;
- int i, j, nre, b;
- char buf[22];
+ ener_file_t in;
+ gmx_bool bCont;
+ gmx_enxnm_t* enm = nullptr;
+ t_enxframe* fr;
+ int i, j, nre, b;
+ char buf[22];
printf("gmx dump: %s\n", fn);
in = open_enx(fn, "r");
if (bCont)
{
- printf("\n%24s %12.5e %12s %12s\n", "time:",
- fr->t, "step:", gmx_step_str(fr->step, buf));
- printf("%24s %12s %12s %12s\n",
- "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
- printf("%24s %12.5e %12s %12s\n",
- "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
+ printf("\n%24s %12.5e %12s %12s\n", "time:", fr->t, "step:", gmx_step_str(fr->step, buf));
+ printf("%24s %12s %12s %12s\n", "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
+ printf("%24s %12.5e %12s %12s\n", "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
if (fr->nre == nre)
{
printf("%24s %12s %12s %12s\n",
- "Component", "Energy", "Av. Energy", "Sum Energy");
+ "Component",
+ "Energy",
+ "Av. Energy",
+ "Sum Energy");
if (fr->nsum > 0)
{
for (i = 0; (i < nre); i++)
{
printf("%24s %12.5e %12.5e %12.5e\n",
- enm[i].name, fr->ener[i].e, fr->ener[i].eav,
+ enm[i].name,
+ fr->ener[i].e,
+ fr->ener[i].eav,
fr->ener[i].esum);
}
}
{
for (i = 0; (i < nre); i++)
{
- printf("%24s %12.5e\n",
- enm[i].name, fr->ener[i].e);
+ printf("%24s %12.5e\n", enm[i].name, fr->ener[i].e);
}
}
}
for (b = 0; b < fr->nblock; b++)
{
- const char *typestr = "";
+ const char* typestr = "";
- t_enxblock *eb = &(fr->block[b]);
- printf("Block data %2d (%3d subblocks, id=%d)\n",
- b, eb->nsub, eb->id);
+ t_enxblock* eb = &(fr->block[b]);
+ printf("Block data %2d (%3d subblocks, id=%d)\n", b, eb->nsub, eb->id);
if (eb->id < enxNR)
{
printf(" id='%s'\n", typestr);
for (i = 0; i < eb->nsub; i++)
{
- t_enxsubblock *sb = &(eb->sub[i]);
+ t_enxsubblock* sb = &(eb->sub[i]);
printf(" Sub block %3d (%5d elems, type=%s) values:\n",
- i, sb->nr, xdr_datatype_names[sb->type]);
+ i,
+ sb->nr,
+ enumValueToString(sb->type));
switch (sb->type)
{
- case xdr_datatype_float:
+ case XdrDataType::Float:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %8.4f\n", j, sb->fval[j]);
}
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10.6f\n", j, sb->dval[j]);
}
break;
- case xdr_datatype_int:
+ case XdrDataType::Int:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10d\n", j, sb->ival[j]);
}
break;
- case xdr_datatype_int64:
+ case XdrDataType::Int64:
for (j = 0; j < sb->nr; j++)
{
- printf("%14d %s\n",
- j, gmx_step_str(sb->lval[j], buf));
+ printf("%14d %s\n", j, gmx_step_str(sb->lval[j], buf));
}
break;
- case xdr_datatype_char:
+ case XdrDataType::Char:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %1c\n", j, sb->cval[j]);
}
break;
- case xdr_datatype_string:
+ case XdrDataType::String:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %80s\n", j, sb->sval[j]);
}
break;
- default:
- gmx_incons("Unknown subblock type");
+ default: gmx_incons("Unknown subblock type");
}
}
}
}
- }
- while (bCont);
+ } while (bCont);
close_enx(in);
sfree(enm);
}
-static void list_mtx(const char *fn)
+//! Dump a (Hessian) matrix file
+void list_mtx(const char* fn)
{
- int nrow, ncol, i, j, k;
- real *full = nullptr, value;
- gmx_sparsematrix_t * sparse = nullptr;
+ int nrow, ncol, i, j, k;
+ real * full = nullptr, value;
+ gmx_sparsematrix_t* sparse = nullptr;
gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
if (full == nullptr)
{
- snew(full, nrow*ncol);
- for (i = 0; i < nrow*ncol; i++)
+ snew(full, nrow * ncol);
+ for (i = 0; i < nrow * ncol; i++)
{
full[i] = 0;
}
{
for (j = 0; j < sparse->ndata[i]; j++)
{
- k = sparse->data[i][j].col;
- value = sparse->data[i][j].value;
- full[i*ncol+k] = value;
- full[k*ncol+i] = value;
+ k = sparse->data[i][j].col;
+ value = sparse->data[i][j].value;
+ full[i * ncol + k] = value;
+ full[k * ncol + i] = value;
}
}
gmx_sparsematrix_destroy(sparse);
{
for (j = 0; j < ncol; j++)
{
- printf(" %g", full[i*ncol+j]);
+ printf(" %g", full[i * ncol + j]);
}
printf("\n");
}
sfree(full);
}
-int gmx_dump(int argc, char *argv[])
+class Dump : public ICommandLineOptionsModule
{
- const char *desc[] = {
- "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
- "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
- "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
- "and prints that to standard output in a readable format.",
- "This program is essential for checking your run input file in case of",
- "problems.[PAR]",
- "The program can also preprocess a topology to help finding problems.",
- "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
- "directories used for searching include files.",
- };
- const char *bugs[] = {
- "Position restraint output from -sys -s is broken"
- };
- t_filenm fnm[] = {
- { efTPR, "-s", nullptr, ffOPTRD },
- { efTRX, "-f", nullptr, ffOPTRD },
- { efEDR, "-e", nullptr, ffOPTRD },
- { efCPT, nullptr, nullptr, ffOPTRD },
- { efTOP, "-p", nullptr, ffOPTRD },
- { efMTX, "-mtx", "hessian", ffOPTRD },
- { efMDP, "-om", nullptr, ffOPTWR }
- };
-#define NFILE asize(fnm)
-
- gmx_output_env_t *oenv;
- /* Command line options */
- gmx_bool bShowNumbers = TRUE;
- gmx_bool bShowParams = FALSE;
- gmx_bool bSysTop = FALSE;
- gmx_bool bOriginalInputrec = FALSE;
- t_pargs pa[] = {
- { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
- { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
- { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" },
- { "-orgir", FALSE, etBOOL, {&bOriginalInputrec}, "Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them" }
+public:
+ Dump() {}
+
+ // From ICommandLineOptionsModule
+ void init(CommandLineModuleSettings* /*settings*/) override {}
+
+ void initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings) override;
+
+ void optionsFinished() override;
+
+ int run() override;
+
+private:
+ //! Commandline options
+ //! \{
+ bool bShowNumbers_ = true;
+ bool bShowParams_ = false;
+ bool bSysTop_ = false;
+ bool bOriginalInputrec_ = false;
+ //! \}
+ //! Commandline file options
+ //! \{
+ std::string inputTprFilename_;
+ std::string inputTrajectoryFilename_;
+ std::string inputEnergyFilename_;
+ std::string inputCheckpointFilename_;
+ std::string inputTopologyFilename_;
+ std::string inputMatrixFilename_;
+ std::string outputMdpFilename_;
+ //! \}
+};
+
+void Dump::initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings)
+{
+ const char* desc[] = { "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
+ "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]tng[tt]), an energy",
+ "file ([REF].edr[ref]), a checkpoint file ([REF].cpt[ref])",
+ "or topology file ([REF].top[ref])",
+ "and prints that to standard output in a readable format.",
+ "This program is essential for checking your run input file in case of",
+ "problems." };
+ settings->setHelpText(desc);
+
+ const char* bugs[] = {
+ "The [REF].mdp[ref] file produced by [TT]-om[tt] can not be read by grompp."
};
+ settings->setBugText(bugs);
+ // TODO If this ancient note acknowledging a bug is still true,
+ // fix it or block that run path:
+ // Position restraint output from -sys -s is broken
+
+ options->addOption(FileNameOption("s")
+ .filetype(OptionFileType::RunInput)
+ .inputFile()
+ .store(&inputTprFilename_)
+ .description("Run input file to dump"));
+ options->addOption(FileNameOption("f")
+ .filetype(OptionFileType::Trajectory)
+ .inputFile()
+ .store(&inputTrajectoryFilename_)
+ .description("Trajectory file to dump"));
+ options->addOption(FileNameOption("e")
+ .filetype(OptionFileType::Energy)
+ .inputFile()
+ .store(&inputEnergyFilename_)
+ .description("Energy file to dump"));
+ options->addOption(
+ FileNameOption("cp").legacyType(efCPT).inputFile().store(&inputCheckpointFilename_).description("Checkpoint file to dump"));
+ options->addOption(
+ FileNameOption("p").legacyType(efTOP).inputFile().store(&inputTopologyFilename_).description("Topology file to dump"));
+ options->addOption(
+ FileNameOption("mtx").legacyType(efMTX).inputFile().store(&inputMatrixFilename_).description("Hessian matrix to dump"));
+ options->addOption(FileNameOption("om")
+ .legacyType(efMDP)
+ .outputFile()
+ .store(&outputMdpFilename_)
+ .description("grompp input file from run input file"));
+
+ options->addOption(
+ BooleanOption("nr").store(&bShowNumbers_).defaultValue(true).description("Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)"));
+ options->addOption(
+ BooleanOption("param").store(&bShowParams_).defaultValue(false).description("Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)"));
+ options->addOption(
+ BooleanOption("sys").store(&bShowParams_).defaultValue(false).description("List the atoms and bonded interactions for the whole system instead of for each molecule type"));
+ options->addOption(
+ BooleanOption("orgir").store(&bShowParams_).defaultValue(false).description("Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them"));
+}
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
- {
- return 0;
- }
-
+void Dump::optionsFinished()
+{
+ // TODO Currently gmx dump ignores user input that seeks to dump
+ // multiple files. Here, we could enforce that the user only asks
+ // to dump one file.
+}
- if (ftp2bSet(efTPR, NFILE, fnm))
+int Dump::run()
+{
+ if (!inputTprFilename_.empty())
{
- list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
- ftp2fn_null(efMDP, NFILE, fnm), bSysTop, bOriginalInputrec);
+ list_tpr(inputTprFilename_.c_str(),
+ bShowNumbers_,
+ bShowParams_,
+ outputMdpFilename_.empty() ? nullptr : outputMdpFilename_.c_str(),
+ bSysTop_,
+ bOriginalInputrec_);
}
- else if (ftp2bSet(efTRX, NFILE, fnm))
+ else if (!inputTrajectoryFilename_.empty())
{
- list_trx(ftp2fn(efTRX, NFILE, fnm));
+ list_trx(inputTrajectoryFilename_.c_str());
}
- else if (ftp2bSet(efEDR, NFILE, fnm))
+ else if (!inputEnergyFilename_.empty())
{
- list_ene(ftp2fn(efEDR, NFILE, fnm));
+ list_ene(inputEnergyFilename_.c_str());
}
- else if (ftp2bSet(efCPT, NFILE, fnm))
+ else if (!inputCheckpointFilename_.empty())
{
- list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
+ list_checkpoint(inputCheckpointFilename_.c_str(), stdout);
}
- else if (ftp2bSet(efTOP, NFILE, fnm))
+ else if (!inputTopologyFilename_.empty())
{
- list_top(ftp2fn(efTOP, NFILE, fnm));
+ list_top(inputTopologyFilename_.c_str());
}
- else if (ftp2bSet(efMTX, NFILE, fnm))
+ else if (!inputMatrixFilename_.empty())
{
- list_mtx(ftp2fn(efMTX, NFILE, fnm));
+ list_mtx(inputMatrixFilename_.c_str());
}
return 0;
}
+
+} // namespace
+
+const char DumpInfo::name[] = "dump";
+const char DumpInfo::shortDescription[] = "Make binary files human readable";
+ICommandLineOptionsModulePointer DumpInfo::create()
+{
+ return std::make_unique<Dump>();
+}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff